1) No you shouldn't need special tools for timing or valve clearenses. The timing marks can be out but not often and not by much. you can feel for top dead center by putting something down a spark plug hole but be careful not to trap it. A degree wheel can even be improvised with a protractor, a wire pointer and a bit of bluetack.
2) Remove front and upper rear engine mounts and drop the engine forwards. Feeler gauges, a good ring spanner and a close fitting screwdriver should be all you need.
3 + 4) HBar master cyl
rear master cyl (front on 254)
Bleeding is easier if you can arrange to have either the master cyl or the caliper uppermost with all the connecting tubes rising in an uninterrupted slope. You do not need any gadgets. Start by putting plenty of absorbent material around then completely undo the bleed nipple. Seal the thread with a bit of brake grease from the rebuild kit and tighten gently. Put a ring spanner on the nipple so it can be tightened and loosened easily. Put a pvc tube on the nipple and position so it loops up 2 or 3 cm before falling to drain into a suitable container. Place something between the pads so that you do not push the pistons out. Keeping the fluid in the master cyl topped up, tighten the nipple, pressurize the system by squeezing the lever, losen the nipple and pump the lever, tighten the nipple, release the lever and repeat.
5) Not easy. Some just accept the 254 as it is. You have the best carbs already.
6) Easier, follow any of the on line guides
I've never yet bought a fancy polishing kit and you've seen my bikes, I would expect even easier results with one. Some alloy corrosion is not going to come good without removing a lot of metal - paint or ice blast this.
7) Easy buy a complete kit and follow the instructions with care...
Thread repair kit with drill
Brackets - paint with a wheel silver or engine bay satin black or zinc plate
Happy to help but I live about 60miles away!